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http://faculty.washington.edu/browning/presto/presto.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)

Proper citation: ENDOG (RRID:SCR_013289) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/

Software application (entry from Genetic Analysis Software)

Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy   

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http://www.brainbank.nl

A biomaterial supply resource which collects, stores, and disseminates diseased and healthy brain tissue. The Netherlands Brain Bank currently contains more than 3600 samples, and each sample includes a neuropathological report and donor medical history. The samples can additionally be matched with ante-mortem parameters and post-mortem parameters upon request. Sample types include cortex, spinal cord, cerebrospinal fluid, plasma, and DNA, among others. Database mining is available with a financial contribution.

Proper citation: Netherlands Brain Bank (RRID:SCR_013841) Copy   

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http://www.openbioinformatics.org/gengen/

A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

Proper citation: GenGen (RRID:SCR_013447) Copy   

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http://www.ncl.ac.uk/ion/about/facilities/nbtr/

A biomaterial supply resource which archives and disseminates brain tissue for the study of normal brain aging and brain disorders. Researchers must create an account in order to browse the database of available tissue. Samples are distributed to researchers in such a way that the identity and personal information of donors is protected.

Proper citation: Newcastle Brain Tissue Resource (RRID:SCR_013843) Copy   

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http://www7.inra.fr/mia/T/MendelSoft/

Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)

Proper citation: MENDELSOFT (RRID:SCR_013177) Copy   

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http://www.flinders.edu.au/sabs/fcas/alsa/alsa_home.cfm

The general purpose of ALSA is to examine how social, biomedical, psychological, economic, and environmental factors are associated with age-related changes in the health and wellbeing of persons aged 70 years and older. The aim is to analyze the complex relationships between individual and social factors and changes in health status, health care needs and service utilization dimensions, with emphasis given to the effects of social and economic factors on morbidity, disability, acute and long-term care service use, and mortality. The study was designed to have common instrumentation with US studies. ALSA collected data from a random, stratified sample of all persons (both community and institution-dwelling) aged 70 years and older living in the metropolitan area of Adelaide, South Australia, using the State Electoral Database as the sampling frame. Spouses aged 65 and older and other household members aged 70 years and older also were invited to participate. The initial baseline data collection for ALSA began in September 1992 and was completed in March 1993. In the first wave, personal interviews were carried out for 2,087 participants, including 566 couples (that is, persons 70 years of age and over and their spouse, if 65 and over). Clinical assessments were obtained for 1,620 of the participants. Respondents were recontacted by telephone a year after initial interview (wave 2). The third wave of the study began in September 1994 and involved a complete reassessment, with a total of 1,679 interviews and 1,423 clinical assessments. To date, eleven waves of data have been collected, with the latest collection in May 2010, from 168 participants. Six of these waves were conducted via face-to-face interviews and clinical assessments, and five were telephone interviews. Future waves are planned, however are dependent on grant funding. Ancillary data collection has been ongoing since the initiation of the study, e.g., from secondary providers. Lists of ALSA participants are compared biannually with the agencies'' lists to determine the prevalence and incidence of receipt of services from these organizations. Another source of information has been the collection of data from the participants'' general practitioners about the respondent''s health status, history of services received, medication use, referrals to specialists, and current services provided. Baseline Sample Size: 2087 Dates of Study: 1992����������2010 (potentially ongoing) Study Features: * Longitudinal * International * Anthropometric Measures * Biospecimens Waves 1-5 (ICPSR), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06707 Wave 6 (ICPSR), http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03679

Proper citation: ALSA - The Australian Longitudinal Study of Ageing (RRID:SCR_013146) Copy   

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http://faculty.washington.edu/browning/beaglecall/beaglecall.html

Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)

Proper citation: BEAGLECALL (RRID:SCR_013301) Copy   

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http://dlin.web.unc.edu/software/spreg-2/

Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)

Proper citation: SPREG (RRID:SCR_013261) Copy   

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http://biomath.med.uth.gr

Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)

Proper citation: HEGESMA (RRID:SCR_013304) Copy   

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http://www.pypop.org/

Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium.

Proper citation: PyPop (RRID:SCR_013425) Copy   

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http://www.multifactordimensionalityreduction.org/

Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software)

Proper citation: MDR (RRID:SCR_013427) Copy   

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http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/

Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software)

Proper citation: ANTMAP (RRID:SCR_013426) Copy   

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http://www.danielsoper.com/statcalc3/

A set of many statistics calculators, including a confidence interval calculator.

Proper citation: Statistics Calculator (RRID:SCR_013827) Copy   

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http://www.gridqtl.org.uk/

Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software)

Proper citation: GRIDQTL (RRID:SCR_013397) Copy   

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http://writefullapp.com

A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail.

Proper citation: Writefull (RRID:SCR_014006) Copy   

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http://www.tcd.ie/IMM/trinity-biobank/index.php

The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).

Proper citation: Trinity Biobank (RRID:SCR_013279) Copy   

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http://www.cns.atr.jp/dni/en/downloads/brain-decoder-toolbox/

Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent.

Proper citation: Brain Decoder Toolbox (RRID:SCR_013150) Copy   

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http://vipbg.vcu.edu/vipbg/trimhap//

Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software)

Proper citation: TRIMHAP (RRID:SCR_013512) Copy   

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http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

•   Source: SciCrunch Registry